Hybrid Proteins with Short Conformational Epitopes of the Receptor-Binding Domain of SARS-CoV-2 Spike Protein Promote Production of Virus-Neutralizing Antibodies When Used for Immunization

Based on the previously developed approach, hybrid recombinant proteins containing short conformational epitopes (a.a. 144-153, 337-346, 414-425, 496-507) of the receptor-binding domain (RBD) of SARS-CoV-2 Spike protein (S protein) were synthesized in Escherichia coli cells as potential components of epitope vaccines. Selected epitopes are involved in protein–protein interactions in the S protein complexes with neutralizing antibodies and ACE2 (angiotensin-converting enzyme 2). The recombinant proteins were used for immunization of mice (three doses with 2-week intervals), and the immunogenicity of protein antigens and ability of the resulting sera to interact with inactivated SARS-CoV-2 and RBD produced in eukaryotic cells were examined. All recombinant proteins showed high immunogenicity; the highest titer in the RBD binding assay was demonstrated by the serum obtained after immunization with the protein containing epitope 414-425. At the same time, the titers of sera obtained against other proteins in the RBD and inactivated virus binding assays were significantly lower than the titers of sera obtained with the previously produced four proteins containing the loop-like epitopes 452-494 and 470-491, the conformation of which was fixed with a disulfide bond. We also studied activation of cell-mediated immunity by the recombinant proteins that was monitored as changes in the levels of cytokines in the splenocytes of immunized mice. The most pronounced increase in the cytokine synthesis was observed in response to the proteins containing epitopes with disulfide bonds (452-494, 470-491), as well as epitopes 414-425 and 496-507. For some recombinant proteins with short conformational epitopes, adjuvant optimization allowed to obtained mouse sera displaying virus-neutralizing activity in the microneutralization assay with live SARS-CoV-2 (hCoV-19/Russia/StPetersburg-3524/2020 EPI_ISL_415710 GISAID). The results obtained can be used to develop epitope vaccines for prevention of COVID-19 and other viral infections.


INTRODUCTION
Development of new vaccines for prevention of COronaVIrus Disease 2019 (COVID 19) and other viral infections is a very important task. Whole virus vaccines, protein subunit and full size protein vaccines, vector based vaccines, and RNA vaccines (which ensure the syn thesis of viral proteins in an organism) induce generation of a wide array of antibodies, although not all of these anti bodies are protective [1]. In some cases, such antibodies can promote antibody dependent enhancement of infec tion when the disease is contracted after vaccination [2 4]. Vaccines containing small epitopes of infectious agent proteins can avoid the abovementioned problems. They are also easily standardized and exhibit low reactogenicity. The drawbacks of epitope vaccines are low immunogenic ity and inability to induce formation of neutralizing anti bodies, as well as possible capacity of new virus variants to avoid immune response developed to these vaccines. Some of the approaches used to increase vaccine immunogenicity and to facilitate the synthesis of virus neutralizing antibodies involve epitope multimeriza tion [5] and adjuvant optimization [6]. Another promising approach is selection of continuous conformational epi topes (elements of protein surface capable of effective induction of antibody synthesis) instead of linear epitopes, since the structure of the former is more similar to the structure of viral protein. Based on the contacts identified in the S protein complexes with neutralizing antibodies and ACE2 (angiotensin converting enzyme 2), we select ed two determinants in the S protein receptor binding motif (RBM) (a.a. 452 494 and 470 491) that participat ed in a large number of contacts between the S protein and neutralizing antibodies or ACE2 [7]. Both determinants have a loop like conformation and include two cysteine residues that form a disulfide bond in the S protein. For immunization, we produced two hybrid proteins, in which the selected antigenic determinants were inserted into the turn of the helix turn helix motif of Methylococcus capsu latus Rop like protein in order to bring together the N and C termini and to preserve the loop like conformation of the epitopes (i.e., the Rop like protein served as an epi tope scaffold). The synthesis of these proteins in Escherichia coli cells and the following purification result ed in the disulfide bond formation in the protein structure [7]. The hybrid proteins also contained the heparin bind ing domain (HBD) to facilitate protein purification and either Thermotoga maritima aldolase (ALD) or α helical fragment (a.a. 958 991) of the SARS CoV 2 S protein to ensure protein trimerization (Tri). High immunogenicity and ability of antibodies formed in response to immuniza tion with these proteins to interact with the S protein receptor binding domain (RBD) and inactivated SARS CoV 2 were demonstrated for all four hybrid proteins.
The objectives of this study were production of other hybrid proteins carrying conformational epitopes of the SARS CoV 2 S protein according to the previously developed protocol, investigation of immunogenicity of the produced proteins and interaction of induced anti bodies with the RBD and inactivated SARS CoV 2, characterization of cytokine response in splenocytes after immunization with the synthesized proteins, investiga tion of virus neutralization by the sera obtained with most promising hybrid proteins in the microneutralization assay with the clinical isolate of SARS CoV 2. Protein purification of soluble and insoluble proteins was carried according to the previously published proto cols [7]. Proteins synthesized as inclusion bodies were sol ubilized in 8 M urea in 10 mM Tris HCl (pH 8.0) and purified on a WorkBeads 40S column (Bio Works, Sweden) equilibrated with 8 M urea in 10 mM Tris HCl (pH 8.0). The proteins were eluted with a linear gradient of NaCl (0 1 M) in the same buffer followed by dialysis against 4 M urea in 25 mM Tris HCl (pH 8.0) for 24 h at 4°C and centrifugation for 30 min at 9000g. Next, the pro teins were subjected to affinity chromatography on heparin Sepharose CL 6B (GE Healthcare, USA) equili brated with 4 M urea in 20 mM Tris HCl (pH 8.0) and eluted with a linear gradient of NaCl (0 1 M) in 4 M urea, 25 mM Tris HCl (pH 8.0) followed by dialysis against 25 mM Tris HCl (pH 6.8) with a stepwise decrease in the urea concentration (to 0 M urea, 0.5 M steps) for 24 h at 4°C. Soluble proteins were purified by chromatography on a WorkBeads 40S column equilibrated with 20 mM Tris HCl (pH 8.0). The proteins were eluted with a linear gradient of NaCl (0 1 M) in the same buffer followed by dialysis against 20 mM Tris HCl (pH 8.0) for 24 h and centrifugation for 30 min at 9000g. Next, affinity chro matography was performed on heparin Sepharose equili brated with 20 mM Tris HCl (pH 8.0). The proteins were eluted with 0 1 M gradient of NaCl in 20 mM Tris HCl (pH 8.0). Obtained protein fractions were dialyzed against 20 mM Tris HCl (pH 8.0), 50 mM NaCl for 24 h at 4°C with three buffer changes.

Strain
The concentration and total amount of protein were determined from the absorbance of protein solutions at 280 nm using bicinchoninic acid. Proteins' preparations were lyophilized and used in further studies.
The molecular mass and theoretical values of some parameters of the recombinant proteins were calculated using the Expasy on line service (https://web.expasy.org/ protparam/). Immunogenic compositions and immunization experi ments. Obtained recombinant proteins (including four previously produced proteins) containing conformational epitopes of SARS CoV 2 S protein were used for prepar ing immunogenic compositions containing 1 nmol of the recombinant protein and respective adjuvant in a single dose (150 μl). In the first experiment, mice were immu nized with seven recombinant proteins (proteins 5 11 in Table 1) mixed with adjuvant 1 containing 1 mg of diethy laminoethyl (DEAE) dextran 500, 75 μl (50%) of mon tanide ISA 201 (Seppic SA, France), and 1.5 μl (1%) of retinol palmitate (100,000 IU/ml; Retinoidy, Russia). The sera produced by immunization were evaluated for the antigen immunogenicity and ability to interact with RBD and inactivated SARS CoV 2 in the first microneu tralization assay and then in splenocytes (cell mediated immunity). The same recombinant proteins were used in the second immunization experiment together with Rop RBM Rop Tri HBD, RBD (Mount Sinai, USA), and previously produced recombinant proteins (proteins 1 4 in Table 1) [7]. Adjuvant 2 added to the immunogenic compositions contained 1 mg of DEAE dextran 500, 0.1 μg of lipopolysaccharide (LPS) of E. coli O55:B5 (Sigma, USA), and 30 μg of CpG oligodeoxynucleotides (ODN 1826) (Evrogen). The produced sera were assayed in the second microneutralization reaction.
Detailed immunization protocols were described in [7]. Female mice (body weight, 18 20 g) of the syn geneic inbred line BALB/c (Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation) were used for immunization at the age of 5 6 weeks. Mice of the experimental group (n = 7) were injected three times every 2 weeks with 150 μl of immunogenic compositions containing recombinant proteins. Animals of the control group (n = 7) were injected with 150 μl of physiological saline. Two weeks after the last injection, mice from the experimental and control groups were anaesthetized by isoflurane inhalation (Piramal Enterprises, India) and their blood was collected from the heart. In the first immunization experiment, we also isolated the spleen in order to evaluate activation of the cell mediated immuni ty (see below). Vacuum tubes with blood samples were incubated at room temperature for 20 min and cen trifuged for 30 min at 1500g without refrigeration. The supernatant (blood serum) was transferred into 1.5 ml sterile tubes and kept frozen at -80°C.
Enzyme linked immunoassay (ELISA). Proteins used for immunization, formaldehyde inactivated SARS CoV 2, and RBD were adsorbed on the microplates and used as antigens in ELISA. Preparation of inactivated SARS CoV 2 and RBD, as well as detailed ELISA proto col, were described in [7]. Briefly, the antigens were adsorbed in 96 well Maxisorp microplates (Thermo Scientific, Denmark) overnight at 4°C. After washing, the plates were incubated for 2 h with blocking buffer (PBS containing 5% fat free milk; TF Ditol, Russia), washed, and incubated with 10 fold serial dilutions of mouse sera. Goat anti mouse IgG (H+L) conjugated with horserad ish peroxidase (Invitrogen, USA) were used as secondary antibodies at 1 : 1200 dilution (100 μl per well). TMB solution (Bioservis, Russia) was used as an HRP substrate for colorimetric detection; the reaction was stopped by Activation of cell mediated immunity was evaluated based on the level of cytokine synthesis by splenocytes from immunized mice using the multiplex immunologi cal assay with the MILLIPLEX MAP Mouse Cytokine/Chemokine Magnetic Bead Panel (Merck Millipore, USA) that allows to measure the levels of 32 regulatory, pro and anti inflammatory cytokines, chemokines, and growth factors [G CSF, GM CSF, IFN γ, IL 1α, IL 1β, IL 2, IL 3, IL 4, IL 5, IL 6, IL 7, IL 9, IL 10, IL 12 (p40), IL 12 (p70), IL 13, IL 15, IL 17, IP 10, KC, LIF, LIX, MCP 1, M CSF, MIG, MIP 1α, MIP 1β, MIP 2, RANTES, TNF α, VEGF, eotaxin/CCL11]. All assays were conducted in accor dance with manufacturer's protocol using recommended sample dilutions and concentrations for the standard curve. The measurements were carried out with a MAG PIX instrument equipped with an xPONENT version 4.2 software (Luminex Corp., USA).
Splenocytes (macrophages, dendritic cells, T and B lymphocytes) were isolated from the mouse spleen 2 weeks after the first immunization experiment. Euthanized mice were washed with 96% alcohol; their abdominal cavity was opened under aseptic conditions; the spleen was isolated and placed into sterile cold DMEM medium (PanEko, Russia). Splenocytes were iso lated using a Tissue Grinder Homogenizer Kit (Sigma). All instruments were sterilized by washing in 96% alcohol followed by flaming. An instrument for tissue disruption was assembled under sterile conditions; 100 and 200 mesh cell sieves (Sigma) were used. The spleen was cut into pieces and passed through the sieve into 9 cm Petri dishes with ice cold DMEM. The resulting cell suspen sion was transferred into 15 ml sterile centrifuge tubes and centrifuged at 200g for 15 min. Pelleted cells were re sus pended in the erythrocyte lysis buffer (150 mM NH 4 Cl, 10 mM KHCO 3 , 1 mM EDTA, pH 7.0 7.6) and incubat ed for 40 s in the dark on ice followed by dilution with ice cold DMEM and centrifugation for 15 min at 200g. The supernatant was discarded and white cell precipitate was resuspended in complete RPMI 1640 medium without glutamine (PanEko) supplemented with 10% FBS (HyClone, USA), 2 mM L glutamine (PanEko), antibiot ic/antimycotic (Sigma), and 0.05 mM 2 mercaptoethanol (Sigma). The cells in the suspension were counted in a Goryaev chamber. The concentration of cell suspension was adjusted to 5 × 10 6 10 7 cell/ml and aliquots (100 μl) were placed into the microplate wells. The cells were in cubated for 1 1.5 h in a CO 2 incubator, after which dilu tions of antigens and controls were introduced into each well. The microplate was incubated for 18 24 h in a CO 2 incubator, after which the culture fluid was transferred into microtubes, frozen, and stored at -80°C prior to analysis. Splenocytes produced in the first immunization experiment (using proteins 5 11 in Table 1 with adjuvant 1) were analyzed simultaneously with spleno cytes isolated after immunization with proteins 1 4 from Table 1 with adjuvant 1 [7] (the plates were stored at -80°C prior to analysis).
Microneutralization assay. Neutralizing antibodies were detected using microneutralization assay based on the Median Tissue Culture Infectious Dose (TCID50) [8]. Mouse sera obtained after three immunization rounds with 2 week intervals were heated for 60 min at 56°C to avoid the complement mediated reduction in the viral activity. Next, a series of 2 fold dilutions of the sera with MEM supplemented with 2% HI FBS was pre pared, starting with 1 : 10 dilution of the whole serum. Each dilution (60 μl) was mixed with an equal volume of the suspension of live SARS CoV 2 (hCoV 19/Russia/ StPetersburg 3524/2020 EPI_ISL_415710 GISAID) containing 25 TCID50/50 μl and incubated for 1 h at 37°C. Next, 100 μl of dilutions were transferred into 96 well plates with a monolayer of Vero cells (ATCC CCL 81). The plates were incubated at 37°C in 5% CO 2 for 4 days and then tested for the cytopathic effect (CPE). Neutralization was registered when 100% cells in the well were preserved, without visible plaques or CPE. The neu tralization titer was calculated as a value reciprocal to the highest dilution for which the neutralizing effect was observed [9].
Experiments on microneutralization were performed in two rounds. In the first microneutralization reaction, we tested the sera obtained in this work and in previous studies [7]  Statistical analysis was performed using Statistica 12.0 package (Statsoft, USA). The normality of distribution was estimated with the Kolmogorov-Smirnov test. The data are presented as mean ± standard deviation (SD) or as geometric mean ± standard geomet ric deviation of logarithm base 2 of the antibody titer in the serum. Statistical significance of differences was eval uated using one way ANOVA with the post hoc Tukey's test. The differences were considered significant at p < 0.05.

Design of recombinant proteins.
Based on the struc ture of SARS CoV 2 S protein in complexes with ACE2 and neutralizing antibodies, four surface epitopes were identified -D4 (a. a. 496 507), D6 (a.a. 144 153), D8  (337 346 a.a.), and D13 (414 425 a.a.) (Fig. 1) -in addi tion to the two previously identified epitopes D2 (a.a. 470 490) and D3 (a.a. 453 494) [7]. All determinants (except D8 with an α helical conformation) had a loop like struc ture with the N and C termini brought close together. Recombinant proteins with the D4, D6, D8, and D13 epi topes were organized similarly to the previously obtained proteins with the D2 and D3 epitopes [7]. All epitopes were flanked with α helices of the Rop like protein from M. capsulatus for additional fixation of N and C termini in order to provide the conformational stability of the epi topes. The loop like determinants were inserted directly into the turn between the helices. In the case of D8 epi tope, flexible glycine containing spacers were introduced between the epitope and α helices of the Rop like pro teins. To ensure multimerization (in this case, trimeriza tion) of epitopes, we used the α helix participating in S protein trimerization (Tri) or ALD from T. maritima (ALD). The recombinant proteins also contained the HBD of HBHA from M. tuberculosis.
Molecular masses of monomeric proteins were in the range of 17 19 kDa (proteins with the Tri sequence) and 35 39 kDa (proteins with the ALD sequence), i.e., were sufficient for the induction of antibody production if trimerization takes place.
The Rop RBM Rop Tri HBD hybrid protein was designed as a control to investigate the virus neutralizing activity of the sera. It contained a fragment of the S pro tein sequence (a.a. 433 511) including D2, D3, and D4 determinants introduced into the turn between the two helices of the Rop like protein.
Synthesis and purification of recombinant proteins. The genes for the recombinant proteins were cloned into the previously generated constructs [7] as described in "Materials and Methods" section. All recombinant pro teins were highly expressed except for Rop D6 Rop ALD HBD, which was omitted from the study. Proteins containing S protein trimerization domain (Tri) were produced as inclusion bodies, while ALD containing proteins were expressed in a soluble form. Therefore, pro tein purification was conducted under denaturing condi tions in the presence of urea (Tri containing proteins) or under non denaturing conditions (proteins with ALD). Chromatography on WorkBeads 40S was used as the first purification step for all proteins; the second purification step was affinity chromatography on heparin Sepharose (because of the presence of HBD in protein structure).
Molecular masses of recombinant proteins calculat ed based on the amino acid sequence and theoretical val ues of some protein parameters are presented in Table 1 (the data for the previously produced proteins with epi topes D2 and D3 [7] are included in Table 1 for compar ison).
The results of electrophoretic separation of purified proteins are shown in Fig. 2 mobility in the presence and absence of reducing agent dithiothreitol (DTT) of proteins with the D2 and D3 epi topes containing two cysteine residues indicates that the purified proteins formed disulfide bonds. The presence of disulfide bond in the proteins with the D2/D3 determi nants was previously demonstrated by mass spectrometry analysis of tryptic peptides [7].
Immunogenic compositions and immunization of mice. Antigenic compositions used for immunization of BALB/C mice were prepared using seven recombinant proteins with the loop like epitopes (proteins 5 11 in Table 1) and adjuvant 1. The presence of specific class G immunoglobulins (IgGs) in the mouse sera was deter mined 2 weeks after three immunizations with 2 week intervals using these proteins, as well as formaldehyde inactivated SARS CoV 2 and RBD, as antigens. Experimental results and the data obtained earlier for the proteins containing D2 and D3 epitopes are presented in Table 2. All hybrid proteins induced formation of high titer IgGs that interacted with the antigens used for immunization. It was shown earlier [7] that proteins con taining D2 and D3 determinants produced high titer antibodies that also interacted with the inactivated virus and RBD. The serum against Rop D13 Rop Tri HBD   also interacted with the RBD. All proteins with the ALD domain, Rop D13 Rop Tri HBD, and Rop D4 Rop Tri HBD were found to be highly immunogenic. The most pronounced response to the RBD was observed with the serum against the Rop D3 Rop ALD HBD protein.
The most pronounced response to inactivated SARS CoV 2 virus was observed for the animals immunized with Rop D2 Rop ALD HBD. Cell mediated immunity. Activation of cell mediated immunity was evaluated by measuring the level of cytokines synthesized by splenocytes of immunized mice. Splenocytes (macrophages, dendritic cells, T and B lym phocytes) isolated from the mouse spleen 2 weeks after immunization with antigens mixed with adjuvant 1 were exposed for 24 h to the same antigens, and their response to the stimulation was estimated from the content of 32 regulatory, pro and anti inflammatory cytokines, chemokines, and growth factors in the growth medium (Fig. 3) The maximal response to Rop D3 Rop ALD HBD (Fig. 3) was in agreement with the maximal titer of anti RBD antibodies demonstrated for this protein (Table 2). Therefore, the highest cellular response was caused by the hybrid proteins Rop D2 Rop Tri HBD, Rop D3 Rop Tri HBD, Rop D2 Rop ALD HBD, Rop D3 Rop ALD HBD, Rop D4 Rop Tri HBD, Rop D4 Rop ALD HBD, and Rop D13 Rop Tri HBD. A ques tion remained whether the antibodies formed in mice after immunization with these proteins exhibited virus neutralizing activity.
Microneutralization reaction. Virus neutralizing antibodies in the sera of immunized mice were detected by the microneutralization assay based on TCID50.
In the first microneutralization reaction, we ana lyzed the sera obtained after the first immunization experiment (three dose immunization with 2 week inter vals, adjuvant 1) and sera obtained previously after immu nization with the proteins carrying D2 and D3 epitopes (adjuvant 1) [7]. None of the tested sera neutralized SARS CoV 2 under assay conditions (see "Materials and Methods" section).
In the second microneutralization reaction, we ana lyzed the sera obtained in the second immunization experiment (three dose immunization with 2 week inter vals, but with adjuvant 2) using recombinant proteins with the investigated epitopes, previously isolated recom binant proteins with the D2 and D3 epitopes [7], Rop RBM Rop Tri HBD, and commercial preparation of RBD (Mount Sinai). The results of microneutralization assay are presented in Table 2. Prevention of the CPE of the live virus (hCoV 19/Russia/StPetersburg 3524/2020 EPI_ISL_415710 GISAID) was observed for some sera dilutions after adjuvant modification, which indicated that specific antibodies capable of neutralizing clinical isolate of the virus were formed in response to immuniza tion with the hybrid proteins containing small antigenic determinants of the SARS CoV 2 S protein. The highest values of the geometric mean titer (GMT) were demon strated for the sera obtained after immunization with Rop D13 Rop Tri HBD (6.7), Rop D2 Rop Tri HBD (7.4), and Rop D4 Rop Tri HBD (8.2). The GMT val ues for the sera obtained by immunization with the con trol preparations of Rop RBM Rop Tri HBD and recombinant RBD were 11.0 and 44.2, respectively ( Table 2).
The N terminal domain (NTD) of the S1 subunit of S protein is limited to the residues 20 286. Several neu tralizing antibodies have been isolated that bind epitopes located in this fragment: 4A8 [16], COV2 2676 and COV2 2489 [17], S2L28, S2M28 and S2X333 [18]. Therefore, designing the constructs with epitopes corre sponding to the NTD (D6) also seems promising.
All epitopes except D8 (α helix) had a loop like conformation in the S protein structure with the N and C termini brought close together. The conformation of the selected epitopes was fixed by inserting them into the turn between the two interacting α helices of the Rop like protein from M. capsulatus. The trimerizing module (either ALD from T. maritima or trimerizing α helix from the S protein) was attached to the construct at the C ter minus. A fragment of hemagglutinin from M. tuberculosis was placed at the C terminus of the construct with the trimerizing module to facilitate purification of hybrid proteins by heparin Sepharose affinity chromatography.  It is interesting to note that despite the fact that all produced hybrid proteins caused formation of high titer IgGs that interacted with the corresponding antigens, only proteins with the D2 and D3 induced antibodies with a titer sufficient for virus inactivation. The antibod ies induced by proteins with the D2 and D3 epitopes and Rop D13 Rop Tri HBD also interacted with the RBD synthesized in prokaryotic cells. The same proteins, as well as Rop D4 Rop ALD HBD and Rop D4 Rop Tri HBD, caused a highly pronounced increase in the level of cytokines in the cell mediated immunity activation assay. The development of innate immune response with poten tial differentiation of B cells was observed as a result of splenocyte stimulation by Rop D3 Rop ALD HBD (and to a lesser degree, by other proteins). We should also mention the presence of very early signs of development of other components of adaptive immune response, in particular, the signs of differentiation of T cells into Th1 cells (IFN γ), as well as appearance of cytokines typical for Th2 and Th17 cells (IL 4, IL 5, and IL 17). The pres ence of stimulatory (IL 1 and IL 12) and suppressor (IL 10) cytokines implies triggering of the full fledged immune response by the antigens. However, despite the pronounced immune response, the sera obtained after immunization of mice with the compositions containing adjuvant 1 displayed no virus neutralizing activity in the microneutralization assay.
Selection of optimal adjuvant in the process of vac cine formulation could be of crucial importance for the development of immune response and formation of pro tective antibodies against certain pathogens [19]. It was found that agonists of the Toll like receptors (TLRs) could be used as adjuvant components to increase the efficiency of UV inactivated vaccine against SARS CoV [20] and vaccine composition based on the recom binant protein containing the ectodomain of the SARS CoV S protein [6]. However, immunization of mice with the ectodomain mixed with gold nanoparticles (adju vant) did not generate protective antibodies [6]. Considering the above information, we modified the adjuvant by replacing montanide ISA 201 and retinol palmitate with TLR agonists -LPS from E. coli O55:B5 and CpG oligodeoxynucleotides (ODN 1826). In the case of adjuvant 2, DEAE dextran 500 (which is present in both adjuvants) also facilitated deposition of CpG oligonucleotides at the site of introduction. Immunization of mice with the hybrid proteins using adjuvant 2 resulted in the generation of sera, some of which ensured efficient neutralization of the clinical iso late of SARS CoV 2 in the microneutralization assay ( Table 2). The most pronounced neutralizing activity was found for the sera produced by immunization with the Rop D13 Rop Tri HBD, Rop D2 Rop Tri HBD, and Rop D4 Rop Tri HBD proteins. Interestingly, all hybrid proteins causing formation of neutralizing anti bodies had a relatively small S protein trimerization domain, rather than the relatively large ALD domain, thus suggesting that the use of smaller protein carriers that shift the ratio towards the dominance of the protein antigenic fragment, could be more productive. It is pos sible that this can be due to the fact that the trimerization domain is a part of the S protein.
Hybrid proteins that caused the most pronounced immune response with the formation of neutralizing anti bodies contained short loop like epitopes located within the RBM boundaries (D2 and D4) or in the RBD region preceding RBM (D13). These epitopes overlap signifi cantly with the linear epitopes S406 420, S475 499, and S495 509 reported by Lu et al. [5] (Fig. 1). According to the data presented in [5], all these linear epitopes are virus neutralizing with respect to the SARS CoV 2 vari ant G614 [5]. This is in good agreement with our results on neutralization of the clinical isolate hCoV 19/Russia/StPetersburg 3524/2020 EPI_ISL_415710 GISAID with the same D614G substitution. The highest ability for the induction of neutralizing antibodies (GMT close to that of the protein with the full size RBM) was found for the protein with the short loop like D4 epitope.
All epitopes selected in this study contained amino acid residues mutated in the S protein of the Omicron variant of SARS CoV 2 (B.1.1.529) that has caused the highest wave of COVID 19 in comparison with the previ ous virus variants [21]. Moreover, most of variable amino acid residues were located in the epitopes with the maxi mal virus neutralizing activity (Fig. 1). This is not sur prising, because all selected determinants are located on the S protein surface, while the RBD region containing all virus neutralizing epitopes is directly involved in the interaction with ACE2. High occurrence of variable sites in the region of neutralizing epitopes would allow to rap idly produce modified sequences based on the existing constructs and to correct the neutralizing response in order to target a corresponding coronavirus mutant. Possibly, it would make sense to expand the boundaries of epitopes and to use entire RBM with the maximal num ber of variable amino acid residues for the development of epitope vaccine. This can be a reasonable approach because RBM contains no glycosylation sites. Recombinant RBM protein is efficiently produced in E. coli; it could be highly purified and subjected to correct re folding with the formation of disulfide bond. It exhibits the highest GMT in the microneutralization assay among all hybrid proteins produced via microbio logical synthesis.
It should be mentioned that despite the results of microneutralization assay, which demonstrate the possi bility of formation of measurable amounts of neutralizing antibodies after immunization with recombinant pro teins carrying small loop like epitopes of the RBD, the GMT values of the obtained sera were lower in compari son with the GMT value for the full size RBD synthe sized in eukaryotic cells. This defines the need for future studies on the development of epitope vaccines for pre vention of coronavirus infection that could include the following directions: (i) search for new promising virus neutralizing epitopes in SARS CoV 2 proteins, e.g., based on the experimental data on linear epitopes that exhibit good correlation with the data on conforma tional epitopes; (ii) combined use of several hybrid pro teins for immunization with varying doses of antigens; (iii) enlargement of loop like epitopes (one of which can be RBM itself); (iv) optimization of epitope multimer ization platform.
Considering that selection of adjuvant to facilitating formation of virus neutralizing antibodies even with very short sequences of the SARS CoV 2 S protein used as antigens, was one of the most significant results of this work, it would be interesting to characterize the immuno genicity of proteins causing formation of neutralizing antibodies, to evaluate the ability of the corresponding for RBD binding and virus inactivation, and to estimate the effect of immunization with these proteins on the cell mediated immunity, which might help in predicting the neutralizing activity of proteins based on simpler experi ments that do not require live virus. This could become another direction of future research.
In conclusion, we demonstrated high immunogenic ity of hybrid recombinant proteins containing small loop like conformational epitopes of RBD and N terminal domain of the SARS CoV 2 S protein. Some of the recombinant proteins induced production of high titer antibodies capable of binding inactivated SARS CoV 2 and RBD synthesized in eukaryotic cells. Activation of cell mediated immunity by immunization with the recombinant proteins was evaluated based on the level of cytokine synthesis by splenocytes from the immunized mice. Modification of the adjuvant, which included introduction of LPS and CpG oligonucleotides (TLR agonists), resulted in the formation of antibodies with the neutralizing activity against live SARS CoV 2 as demon strated by the microneutralization assay.
Funding. This work was supported by the Russian Foundation for Basic Research (project no. 20 04 60373\20). Production of the Rop RBM Rop Tri HBD protein and investigation of its ability to induce formation of virus neutralizing antibodies was supported by the State Budget Project of the Ministry of Health of the Russian Federation (project no. 056 00119 21 00, Development of the ACE2 receptor blocker for preven tion and therapy of coronavirus infection).
Ethics declarations. The authors declare no conflicts of interest in financial or any other sphere. All applicable international, national, and/or institutional guidelines for the care and use of animals have been followed.
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